4HCR

Crystal structure of human MAdCAM-1 D1D2 complexed with Fab PF-547659

• PDB DOI: https://doi.org/10.2210/pdb4HCR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2012-10-01 Released: 2013-01-23 
• Deposition Author(s): Springer, T., Yu, Y., Zhu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.208 
• R-Value Work: 0.153 
• R-Value Observed: 0.158 

Literature

A Different Fold with an Integrin-Binding Loop Specialized for Flexibility in Mucosal Addressin Cell Adhesion Molecule-1

Springer, T., Yu, Y., Zhu, J., Wang, J.-H., Huang, P.-S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 142 kDa 
• Atom Count: 10,592 
• Modelled Residue Count: 1,258 
• Deposited Residue Count: 1,314 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PF-547659 heavy chain	A [auth H], D [auth M]	229	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PF-547659 light chain	B [auth L], E [auth N]	219	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucosal addressin cell adhesion molecule 1	C [auth A], F [auth B]	209	Homo sapiens	Mutation(s): 1  Gene Names: MADCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13477 (Homo sapiens) Explore Q13477  Go to UniProtKB:  Q13477
PHAROS:  Q13477 GTEx:  ENSG00000099866

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.208 
• R-Value Work: 0.153 
• R-Value Observed: 0.158 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.94	α = 90
b = 112.26	β = 89.95
c = 157.92	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Springer, T., Yu, Y., Zhu, J.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2021-05-26
  Changes: Database references, Source and taxonomy
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Structure summary